Except we never had those three fighting in the same team already, not to mention Isa and Braig would be surely around as well.
And they could even go the 13 vs. 7 concept (which while I accept it still rubs me the wrong way compared to the BBS-method, as gathering 7 and 13 hearts which can even be replaced may be more strenuous, but is certainly easier than creating pure hearts of one element and nurture them) without using Time Travel by simply using present people.
The most eerie problem with the "thirteen" Xehanorts right now would be that there's at least one (Terra), possibly two or three (depending on Isa's true stance and if Eraqus is a darkness too) of them who the heroes actually want back on their side instead of defeating them.
If it was Sora, Riku, Mickey and Lea - and at least Aqua, if not the rest of the people in torment - against MX, Ansem, Xemnas and his lackies, it wouldn't be particularly miraculous if they won. I think there's more room for mystery and expansion on the concepts of KH this way.
And yet still there are many people out who call it an "asspull" or retcon despite it being hinted at during the whole series since CoM. That's either willing denial or Nomura didn't quite illustrate it enough to be hammered home.
Most likely the people who paid the "spin-offs" no heed. Though, to be fair, KHII did a poor job of highlighting the true nature of the heart, making it seem like more of an object at times.
There is no real "concept" of fate. Xehanort manufactures "fate" with his constant plans which try to upset the balance of the universe, so it's not really "fate" at all. Besides, we don't need Lea for that as Xehanort repeatedly dismissed the influence of free will in his schemes and got kicked in the butt because of that.
Despite so many backup plans and elaborate schemes, while he may be still around, so far everyone of Xehanort's schemes failed in the end. That's why he needs that many backup plans.
Were the use of "fate" employed in a similar fashion to your typical shounen manga (i.e. calling tradition or the most probable outcome "fate"), then I would be inclined to agree. In this case, "fate" is a part of temporal logic. When someone from the future arrives in your time, it has been predetermined that that person will go back in time. I believe this is the core of what fate means to the series, even though Xehanort tries to use it to justify his acts.
Altering history would be not a good way to end it in my opinion, as then Terra and Aqua would never befriend Ventus, who would remain a lonely orphan in some lackluster world, Kairi would never come to Destiny Islands, Roxas, Xion and Naminé would never be born and Sora as well as all the others (Lea, Donald, Goofy etc.) would never make all the friends and bonds they did over the course of the series.
Or, tl;dr: Every game in the series sans KH 3 would become meaningless because it never happened. Cosmic retcon extraordinaire which would destroy also everything good that was build up over the series including the three main trios.
The idea is that all bonds, memories and even hearts conceived would remain the same, except those related to Xehanort. No one would really know the people that they had originally met, but they would still end up being pulled towards each other by their bonds. Roxas, Xion and Namine would be their own people and hang out with the Twilight Town gang.
The potential for the Replica project is definitely greater than they actually showed. Replicas have a heart already (or grow one) and therefore can become their own persons as well (as seen with Replica Riku and Xion), just like in Real Life a clone may be genetically identical but it's never the exact same person than the "template".
Seeing that Xehanort needs "vessels" aka bodies, aka at least some physical shell for his heart seeds to occupy, the Replica project could very well be a source for vessels, would Xehanort spare the effort to "de-heart" existing people and just place a heart seed inside a Replica before it can grow its own heart.
Good point, but Xehanort doesn't have Even/Vexen on his side anymore, or so it seems. During the good ol' days of Organization XIII, Xemnas was probably hoping to experiment more with the Replicas before deciding to use them as a backup plan.